Hi Ross,
Only PCI-E gen 3 x 16 slots? What about PCI-E gen 2 x 16 slots?
Regards,
Filip
On Wednesday, March 12, 2014 12:25 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
Hi Kshatresh,
What do you mean by double computational efficiency? For GPU AMBER the
performance is determined almost exclusively (with a few minor caveats) by
the GPU. AMBER 14 will be about 30% faster than AMBER 12 across the board
for PME calculations - substantially faster for NPT if you use the new
Monte Carlo Barostat. It will also support peer to peer across 2 x 2 GPUs
on most motherboards. That is you can run peer to peer parallel on GPUs
connected to the same IOH controller - which effectively means CPU socket
as long as those cards are on PCI-E gen 3 x 16 slots or better. 4 way peer
to peer will be supported at some point (the code will support it
natively) but the hardware itself does not exist yet (we are ahead of the
hardware curve for once! :-) ).
Let me know some more details about what you want to simulate, the sort
performance you are after and I can let you know what GPU models, what
settings etc to try. Note AMBER 14 will also support hydrogen mass
repartitioning so in principal you can run at 4fs time step. This gets you
to around 380+ ns/day for a JAC NPT run (4fs) with two GTX-Titan-Blacks. -
Note we are waiting on a fix from NVIDIA before the Titan Black will
actually be usable with AMBER - at present calculations diverge or crash
within about 15 minutes or so. I am confident that a fix will be possible
though (it was for the original Titans so stay tuned).
All the best
Ross
On 3/11/14, 2:35 PM, "Kshatresh Dutta Dubey" <kshatresh.gmail.com> wrote:
>Thank you Dr. Ross, I will contact Mike for desired configurations.
>Although I have previous quote for Model Quantum TXR413-512R but I need
>almost double computational efficiency relative to that one.
>Regards
>Kshatresh
>
>
>On Tue, Mar 11, 2014 at 9:31 PM, Ross Walker <ross.rosswalker.co.uk>
>wrote:
>
>> Hi Kshatresh
>>
>> Let me put you in touch with Mike Chen at Exxact Corp (cc'd here).
>>Exxact
>> are our hardware partners for building AMBER Certified GPU machines.
>>They
>> can quote you a system that is optimized price/performance wise for
>> running AMBER. It will ship fully tested, certified and warrantied. They
>> can also customize the machine to your specific requirements and budget.
>>
>> Please see the following pages:
>> http://ambermd.org/gpus/recommended_hardware.htm#hardware
>>
>> and
>>
>> http://exxactcorp.com/index.php/solution/solu_list/65
>>
>> for more info.
>>
>> All the best
>> Ross
>>
>>
>>
>>
>>
>>
>> On 3/11/14, 9:46 AM, "Kshatresh Dutta Dubey" <kshatresh.gmail.com>
>>wrote:
>>
>> >Dear all,
>> >
>> >We have to purchase GPU machine suitable for next release of Amber
>>14. We
>> >have to run the MD simulations for a large system (about 100K atom). I
>> >will
>> >be thankful if someone suggests me for the best configurations. Our
>>grant
>> >allows us for 20K USD.
>> >Thanks in advance
>> >Kshatresh
>> >
>> >--
>> >_______________________________________________
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>> >AMBER.ambermd.org
>> >http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
>--
>With best regards
>**************************************************************************
>**********************
>Dr. Kshatresh Dutta Dubey
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
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Received on Tue Mar 11 2014 - 16:00:02 PDT
